Hello!
I'm new to the field of Bioinformatics (I'm studying Molecular Biology in my 3rd year) and I'm currently doing an internship at a company.
I got FastQ and FASTA (Pacbio) files and should do a de-novo assambly (of Aeromonas salmonicida pectinolytica) with them. The files are 400mb each and have about 68.000 reads size 35-18.000 bases. I first tried the pacbio smrtanalays/portal tool. But I need bad.h5 data for this, which i don't have. So I am now using Mira 4.0.
Syntax:
Manifest:
output:
But it fails every time. It sounds like mira doesn't recognize the technology..i also tried pcbiohq which also did't work!
Thank you very much everyone for your help. I'm a really beginner in this topic.
I'm new to the field of Bioinformatics (I'm studying Molecular Biology in my 3rd year) and I'm currently doing an internship at a company.
I got FastQ and FASTA (Pacbio) files and should do a de-novo assambly (of Aeromonas salmonicida pectinolytica) with them. The files are 400mb each and have about 68.000 reads size 35-18.000 bases. I first tried the pacbio smrtanalays/portal tool. But I need bad.h5 data for this, which i don't have. So I am now using Mira 4.0.
Syntax:
./mira manifest.conf>log_assembly.txt
project = MyFirstAssembly
job = genome,denovo,draft
parameters = PCBIOHQ_SETTINGS -CO:mrpg=5
readgroup = L4466_Track data = XX.fastq XX2.fastq technology = sanger
segment_placement= FR
job = genome,denovo,draft
parameters = PCBIOHQ_SETTINGS -CO:mrpg=5
readgroup = L4466_Track data = XX.fastq XX2.fastq technology = sanger
segment_placement= FR
On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012 x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux annapurna 3.13.0-29-generic #53-Ubuntu SMP Wed Jun 4 21:00:20 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Oooops, the readgroup 'L4466_Track data = XX.fastq *
* XX2.fastq technology=sanger' has no sequencing *
* technology defined, nor is it defined as reference (which would excuse the *
* missing technology definition). *
********************************************************************************
->Thrown: void ReadGroupLib::fillInSensibleDefaults(rgid_t libid)
->Caught: main
Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see: http://www.freelists.org/list/mira_talk
CWD: /home/haudum/Project/Program/Mira/mira_4.0.2_linux-gnu_x86_64_static/bin
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Your system seems to be older or have some quirks with locale settings.
Using the LC_ALL=C workaround.
If you don't want that, fix your system ;-)
Failure, wrapped MIRA process aborted.
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux annapurna 3.13.0-29-generic #53-Ubuntu SMP Wed Jun 4 21:00:20 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Oooops, the readgroup 'L4466_Track data = XX.fastq *
* XX2.fastq technology=sanger' has no sequencing *
* technology defined, nor is it defined as reference (which would excuse the *
* missing technology definition). *
********************************************************************************
->Thrown: void ReadGroupLib::fillInSensibleDefaults(rgid_t libid)
->Caught: main
Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see: http://www.freelists.org/list/mira_talk
CWD: /home/haudum/Project/Program/Mira/mira_4.0.2_linux-gnu_x86_64_static/bin
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Your system seems to be older or have some quirks with locale settings.
Using the LC_ALL=C workaround.
If you don't want that, fix your system ;-)
Failure, wrapped MIRA process aborted.
Thank you very much everyone for your help. I'm a really beginner in this topic.
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